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Detailed information for vg0514034074:

Variant ID: vg0514034074 (JBrowse)	Variation Type: SNP
Chromosome: chr05	Position: 14034074
Reference Allele: G	Alternative Allele: A
Primary Allele: G	Secondary Allele: A

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATCCTCGTCCAGGAATCAGCCGAGGTACACAAACTAACAATTTAATATAAAAATCCATCATAATAATAACGTTACATACTTACAAAAGAAAAGAAAAACA[G/A]
CAGCGGAATTAACGGTCTAGCAATGGCTTCAGCTCCATTCCCACAGGCAGCTCAACTGGGGTATAAGCCAAACGTCTTCTCCTTCTGGATCCTTTCTCTT

Reverse complement sequence

AAGAGAAAGGATCCAGAAGGAGAAGACGTTTGGCTTATACCCCAGTTGAGCTGCCTGTGGGAATGGAGCTGAAGCCATTGCTAGACCGTTAATTCCGCTG[C/T]
TGTTTTTCTTTTCTTTTGTAAGTATGTAACGTTATTATTATGATGGATTTTTATATTAAATTGTTAGTTTGTGTACCTCGGCTGATTCCTGGACGAGGAT

Allele Frequencies:

Populations	Population Size	Frequency of G(primary allele)	Frequency of A(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	93.60%	4.10%	0.85%	1.46%	NA
All Indica	2759	89.20%	7.00%	1.41%	2.46%	NA
All Japonica	1512	99.90%	0.10%	0.07%	0.00%	NA
Aus	269	99.60%	0.00%	0.00%	0.37%	NA
Indica I	595	77.50%	9.90%	3.70%	8.91%	NA
Indica II	465	97.80%	1.50%	0.65%	0.00%	NA
Indica III	913	91.90%	7.70%	0.33%	0.11%	NA
Indica Intermediate	786	89.70%	7.10%	1.40%	1.78%	NA
Temperate Japonica	767	100.00%	0.00%	0.00%	0.00%	NA
Tropical Japonica	504	100.00%	0.00%	0.00%	0.00%	NA
Japonica Intermediate	241	99.20%	0.40%	0.41%	0.00%	NA
VI/Aromatic	96	100.00%	0.00%	0.00%	0.00%	NA
Intermediate	90	100.00%	0.00%	0.00%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg0514034074	G -> DEL	N	N	silent_mutation	Average:53.781; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0514034074	G -> A	LOC_Os05g24250.1	upstream_gene_variant ; 4750.0bp to feature; MODIFIER	silent_mutation	Average:53.781; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0514034074	G -> A	LOC_Os05g24260.1	downstream_gene_variant ; 2712.0bp to feature; MODIFIER	silent_mutation	Average:53.781; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0514034074	G -> A	LOC_Os05g24270.1	downstream_gene_variant ; 950.0bp to feature; MODIFIER	silent_mutation	Average:53.781; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N
vg0514034074	G -> A	LOC_Os05g24270-LOC_Os05g24280	intergenic_region ; MODIFIER	silent_mutation	Average:53.781; most accessible tissue: Zhenshan97 flag leaf, score: 76.061	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg0514034074	1.97E-06	NA	mr1961_2	Ind_All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251